Diffusion models have seen wide adoption for 3D molecular generation, yet they offer no principled signal of when a generated molecule is likely to be of low quality. We propose a post-hoc method for estimating per-sample uncertainty in pretrained molecular diffusion models.
arXiv:2606. 01595v1 Announce Type: new Abstract: Bayesian inference provides a principled framework for modeling epistemic uncertainty in neural networks by treating predictions as distributions rather than deterministic values.
arXiv:2606. 13955v1 Announce Type: new Abstract: Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples.
arXiv:2512.20003v2 Announce Type: replace Abstract: Sampling from unnormalized probability densities is a pervasive challenge across the computational and physical sciences. Diffusion models provide...
We introduce the Intrinsic Hybrid Latent Diffusion Model (ILDM), a generative framework that integrates probabilistic dimensionality reduction with geometry-aware diffusion on unknown manifolds. While diffusion models (DMs) have achieved state-of-the-art results in high-dimensional data synthesis, they rely on large training datasets and ignore intrinsic geometric structure.
arXiv:2607. 09277v1 Announce Type: new Abstract: Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori.
arXiv:2608. 04827v1 Announce Type: cross Abstract: We introduce the Intrinsic Hybrid Latent Diffusion Model (ILDM), a generative framework that integrates probabilistic dimensionality reduction with geometry-aware diffusion on unknown manifolds.
arXiv:2604. 17838v2 Announce Type: replace Abstract: Generative modeling within constrained sets is essential for scientific and engineering applications involving physical, geometric, or safety requirements (e.
Transport-Coupled Bayesian Flows for Molecular Graph Generation (TopBF) addresses a key mismatch in existing diffusion models for molecular graph generation by eliminating the need for hard discretization during sampling. The framework generates graphs directly in continuous parameter distributions, learns graph topology via a Quasi-Wasserstein optimal‑transport coupling with geodesic costs, and enables property‑conditioned generation without retraining. Experiments on QM9 and ZINC250k show that TopBF achieves higher structural fidelity and more efficient generation compared to prior methods.
arXiv:2609.00955v1 Announce Type: new Abstract: Diffusion models achieve strong image generation quality but incur high iterative denoising costs. Analog compute-in-memory (CIM) can accelerate matrix...
arXiv:2606. 01086v1 Announce Type: cross Abstract: Flow and diffusion models generate high-quality samples in many modalities; however, many network evaluations are required during inference due to numerical integration of an underlying differential equation.
arXiv:2607. 07232v1 Announce Type: cross Abstract: Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design.
Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design. Yet, scaling these models to large graphs remains an open problem.